edit: Thanks to anyone who read this. I deleted the changelog file and the distfiles for the package then ran emerge -av sys-devel/llvm and it got past the point of failure. It's working now so I've marked this as solved.

I had the one file cause a problem, as in the original post. It was just a changelog, so I deleted it- Worst case scenario I have to delete and rebuild the /usr/portage tree from a tarball...
Everything started merging again, until I had to quit the process (I had a package that wouldn't merge, so I shut the computer down when it died).
Later on, I had the computer at home, and without running emerge --sync, I simply ran

Code:

emerge -av kde-meta

I had 20+ more of the same failures- all of them on the ChangeLog file for their respective package.

A few notes:

All except for the last 2 of ExecutorElassus' packages were on my list of problematic packages... obviously there were quite a few more, but my emerge was 488 packages.

@EE: I did some reading on this- according to official Getoo sources, resyncing the tree in response to this problem is likely to make the problem worse, not better.